import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Vector;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-import jalview.analysis.SecStrConsensus;
import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import fr.orsay.lri.varna.factories.RNAFactory;
import fr.orsay.lri.varna.models.rna.RNA;
-/**
- * @author jimp
- *
- */
-public class RnamlFile extends AlignFile {
- public int id;
- public String namefile;
- public String name;
- protected ArrayList<RNA> result;
-
- public RnamlFile() {
- super();
-
- }
-
- public RnamlFile(String inFile, String type) throws Exception {
- super(inFile, type);
-
- }
-
- public RnamlFile(FileParse source) throws Exception {
- super(source);
-
- }
-
- public BufferedReader CreateReader() throws FileNotFoundException {
- FileReader fr = null;
- fr = new FileReader(inFile);
-
- BufferedReader r = new BufferedReader(fr);
- return r;
- }
-
- /* (non-Javadoc)
- * @see jalview.io.AlignFile#parse()
- */
- public void parse() throws IOException
- {
- // rather than lose exception semantics whilst parsing RNAML with VARNA we
- // wrap the routine and catch all exceptions before passing them up the
- // chain as an IOException
- try {
- _parse();
- } catch (Exception x)
- {
- error=true;
- errormessage="Problem parsing data as RNAML ("+x.getMessage()+")";
- throw new IOException("Couldn't parse the datasource as RNAML",x);
- }
- }
- @SuppressWarnings("unchecked")
- public void _parse() throws FileNotFoundException,
- ExceptionPermissionDenied, ExceptionLoadingFailed,
- ExceptionFileFormatOrSyntax {
-
- result = RNAFactory.loadSecStrRNAML(getReader());
-
- ArrayList<ArrayList> allarray = new ArrayList();
- ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
- ArrayList strucinarray = new ArrayList();
- SequenceI[] seqs = new SequenceI[result.size()];
- namefile = inFile.getName();
-
- for (int i = 0; i < result.size(); i++) {
-
- RNA current = result.get(i);
- String rna = current.getStructDBN(true);
- String seq = current.getSeq();
- int begin = 1;
- int end = 1000;
- id = i;
- System.out.println("id=" + i);
- name = this.safeName(namefile, i);
- seqs[i] = new Sequence(name, seq, begin, end);
-
- seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
- String[] annot = new String[rna.length()];
- Annotation[] ann = new Annotation[rna.length()];
-
- for (int j = 0; j < rna.length(); j++) {
- annot[j] = "" + rna.charAt(j);
-
- }
- for (int k = 0; k < rna.length(); k++) {
- ann[k] = new Annotation(annot[k], "",
- jalview.schemes.ResidueProperties.getRNASecStrucState(
- annot[k]).charAt(0), 0f);
- }
-
- AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
- current.getID(), ann);
-
- seqs[i].addAlignmentAnnotation(align);
- seqs[i].setRNA(result.get(i));
-
- char[] struc = align.getRNAStruc().toCharArray();
-
- allarray.add(strucinarray);
-
- this.annotations.addElement(align);
- BP.add(align.bps);
-
- }
- this.setSeqs(seqs);
- int[] tab = SecStrConsensus.extractConsensus(BP);
-
-
- }
-
- public void parse(BufferedReader r) throws ExceptionPermissionDenied,
- ExceptionLoadingFailed, ExceptionFileFormatOrSyntax {
-
- result = RNAFactory.loadSecStrRNAML(r);
-
- ArrayList<ArrayList> allarray = new ArrayList();
- ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
- ArrayList strucinarray = new ArrayList();
- SequenceI[] seqs = new SequenceI[result.size()];
- namefile = inFile.getName();
-
- for (int i = 0; i < result.size(); i++) {
-
- RNA current = result.get(i);
- String rna = current.getStructDBN(true);
-
- String seq = current.getSeq();
- int begin = 1;
- int end = 1000;
- id = i;
- name = this.safeName(namefile, i);
- seqs[i] = new Sequence(name, seq, begin, end);
-
- seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
- String[] annot = new String[rna.length()];
- Annotation[] ann = new Annotation[rna.length()];
-
- for (int j = 0; j < rna.length(); j++) {
- annot[j] = "" + rna.charAt(j);
-
- }
- for (int k = 0; k < rna.length(); k++) {
- ann[k] = new Annotation(annot[k], "",
- jalview.schemes.ResidueProperties.getRNASecStrucState(
- annot[k]).charAt(0), 0f);
- }
-
- AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
- current.getID(), ann);
-
- seqs[i].addAlignmentAnnotation(align);
- seqs[i].setRNA(result.get(i));
-
- char[] struc = align.getRNAStruc().toCharArray();
- for (int y = 0; y < struc.length; y++) {
- strucinarray.add(struc[y]);
- // System.out.println("structy"+struc[y]);
- }
- // System.out.println("Sequence"+i+"\t : "+strucinarray.toString());
- allarray.add(strucinarray);
-
- this.annotations.addElement(align);
- System.out.println(rna);
- BP.add(align.bps);
- System.out.println(align.bps.size());
- }
- this.setSeqs(seqs);
- int[] tab = SecStrConsensus.extractConsensus(BP);
-
-
- }
-
-
-
- public static String print(SequenceI[] s) {
- return "not yet implemented";
- }
-
- public String print() {
- System.out.print("print :");
- return print(getSeqsAsArray());
- }
-
- public ArrayList getRNA() {
- return result;
- }
-
- public Vector getAnnot() {
- return annotations;
- }
-
- // public static void main(String[] args) {
- // Pattern p= Pattern.compile("(.+)[.][^.]+");
- // Matcher m = p.matcher("toto.xml.zip");
- // System.out.println(m.matches());
- // System.out.println(m.group(1));
- // }
- public String safeName(String namefile, int id) {
-
- Pattern p = Pattern.compile("(.*)[.][^.]+");
- Matcher m = p.matcher(namefile);
- name = m.group(1) + "_" + id;
-
- return name;
-
- }
-
+public class RnamlFile extends AlignFile
+{
+ public String id;
+
+ protected ArrayList<RNA> result;
+
+ public RnamlFile()
+ {
+ super();
+
+ }
+
+ public RnamlFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+
+ }
+
+ public RnamlFile(FileParse source) throws IOException
+ {
+ super(source);
+
+ }
+
+ public BufferedReader CreateReader() throws FileNotFoundException
+ {
+ FileReader fr = null;
+ fr = new FileReader(inFile);
+
+ BufferedReader r = new BufferedReader(fr);
+ return r;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.AlignFile#parse()
+ */
+ public void parse() throws IOException
+ {
+ if (System.getProperty("java.version").indexOf("1.6") > -1
+ || System.getProperty("java.version").indexOf("1.5") > -1)
+ {
+ // patch for 'This parser does not support specification "null" version
+ // "null"' error
+ // this hack ensures we get a properly updated SAXParserFactory on older
+ // JVMs
+ // thanks to Stefan Birkner over at https://coderwall.com/p/kqsrrw
+ System.setProperty("javax.xml.parsers.SAXParserFactory",
+ "com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl");
+ }
+ // rather than lose exception semantics whilst parsing RNAML with VARNA we
+ // wrap the routine and catch all exceptions before passing them up the
+ // chain as an IOException
+ try
+ {
+ _parse();
+ } catch (ExceptionPermissionDenied pdx)
+ {
+ errormessage = "Couldn't access datasource (" + pdx.getMessage()
+ + ")";
+ throw new IOException(pdx);
+ } catch (ExceptionLoadingFailed lf)
+ {
+ errormessage = "Couldn't process data as RNAML file ("
+ + lf.getMessage() + ")";
+ throw new IOException(lf);
+ } catch (ExceptionFileFormatOrSyntax iff)
+ {
+ errormessage = "Invalid RNAML file (" + iff.getMessage() + ")";
+ throw new IOException(iff);
+ } catch (Exception x)
+ {
+ error = true;
+ errormessage = "Problem parsing data as RNAML (" + x.getMessage()
+ + ")";
+ throw new IOException("Couldn't parse the datasource as RNAML", x);
+ }
+ }
+
+ @SuppressWarnings("unchecked")
+ public void _parse() throws FileNotFoundException,
+ ExceptionPermissionDenied, ExceptionLoadingFailed,
+ ExceptionFileFormatOrSyntax
+ {
+
+ result = RNAFactory.loadSecStrRNAML(getReader());
+
+ ArrayList<ArrayList> allarray = new ArrayList();
+ ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
+ ArrayList strucinarray = new ArrayList();
+ SequenceI[] seqs = new SequenceI[result.size()];
+
+ for (int i = 0; i < result.size(); i++)
+ {
+
+ RNA current = result.get(i);
+ String rna = current.getStructDBN(true);
+ String seq = current.getSeq();
+ int begin = 1;
+ int end = seq.length();
+
+ id = current.getName();
+ seqs[i] = new Sequence(id, seq, begin, end);
+
+ seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
+ String[] annot = new String[rna.length()];
+ Annotation[] ann = new Annotation[rna.length()];
+
+ for (int j = 0; j < rna.length(); j++)
+ {
+ annot[j] = "" + rna.charAt(j);
+
+ }
+ for (int k = 0; k < rna.length(); k++)
+ {
+ ann[k] = new Annotation(annot[k], "",
+ jalview.schemes.ResidueProperties.getRNASecStrucState(
+ annot[k]).charAt(0), 0f);
+ }
+
+ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
+ current.getID(), ann);
+
+ seqs[i].addAlignmentAnnotation(align);
+ seqs[i].setRNA(result.get(i));
+
+ allarray.add(strucinarray);
+
+ annotations.addElement(align);
+ BP.add(align.bps);
+
+ }
+
+ setSeqs(seqs);
+ }
+
+ public static String print(SequenceI[] s)
+ {
+ return "not yet implemented";
+ }
+
+ public String print()
+ {
+ System.out.print("print :");
+ return print(getSeqsAsArray());
+ }
+
+ public ArrayList getRNA()
+ {
+ return result;
+ }
+
+ // public static void main(String[] args) {
+ // Pattern p= Pattern.compile("(.+)[.][^.]+");
+ // Matcher m = p.matcher("toto.xml.zip");
+ // System.out.println(m.matches());
+ // System.out.println(m.group(1));
+ // }
+ /**
+ * make a friendly ID string.
+ *
+ * @param dataName
+ * @return truncated dataName to after last '/'
+ */
+ private String safeName(String dataName)
+ {
+ int b = 0;
+ while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
+ {
+ dataName = dataName.substring(b + 1).trim();
+
+ }
+ int e = (dataName.length() - dataName.indexOf(".")) + 1;
+ dataName = dataName.substring(1, e).trim();
+ return dataName;
+ }
}
git://source.jalview.org / jalview.git / commitdiff